[MODIF] update cooltools

conf/modules.config

@@ -204,4 +204,23 @@ process {
     ]
     ext.args = "--balance"
   }
-}
+
+  //********************************
+  // COMPARTMENTS
+
+  withName: 'CALL_COMPARTMENTS' {
+    ext.args = '--bigwig'
+  }
+
+  //********************************
+  // TADS
+
+  withName: 'INSULATION' {
+    ext.args = '15 25 50 --window-pixels'
+  }
+
+  withName: 'HIC_FIND_TADS' {
+    ext.args = '--correctForMultipleTesting fdr'
+  }
+
+}
\ No newline at end of file

modules/local/compartment_calling.nf

-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options    = initOptions(params.options)
-
-process compartment_calling {
-  tag "$sample - $res"
-  label 'process_medium'
-  publishDir "${params.outdir}/compartments", mode: 'copy'
-
-  when:
-  !params.skip_compartments
-
-  input:
-  tuple val(sample), val(res), path(cool), val(r) 
-  path(fasta) 
-  path(chrsize) 
-
-  output:
-  path("*compartments*") optional true, emit:out_compartments
-
-  script:
-  """
-  cooltools genome binnify --all-names ${chrsize} ${res} > genome_bins.txt
-  cooltools genome gc genome_bins.txt ${fasta} > genome_gc.txt 
-  cooltools call-compartments --contact-type cis -o ${sample}_compartments ${cool}
-  awk -F"\t" 'NR>1{OFS="\t"; if(\$6==""){\$6=0}; print \$1,\$2,\$3,\$6}' ${sample}_compartments.cis.vecs.tsv | sort -k1,1 -k2,2n > ${sample}_compartments.cis.E1.bedgraph
-  """
-}

modules/local/cooltools/eigs-cis.nf

+/*
+ * cooltools - call_compartments
+ */
+ 
+process CALL_COMPARTMENTS {
+  label 'process_medium'
+
+  input:
+  tuple val(meta), val(res), path(cool)
+  path(fasta) 
+  path(chrsize) 
+
+  output:
+  path("*compartments*"), emit: results
+  path("versions.yml"), emit: versions
+
+  script:
+  def args = task.ext.args ?: ''
+  def prefix = task.ext.prefix ?: "${meta.id}"
+  """
+  cooltools genome binnify --all-names ${chrsize} ${res} > genome_bins.txt
+  cooltools genome gc genome_bins.txt ${fasta} > genome_gc.txt 
+  cooltools eigs-cis ${args} -o ${prefix}_compartments ${cool}
+
+  cat <<-END_VERSIONS > versions.yml
+  "${task.process}":
+      cooltools: \$(cooltools --version 2>&1 | sed 's/cooletools, version //')
+  END_VERSIONS
+  """
+}

modules/local/cooltools/insulation.nf

+/*
+ * Cooltools - diamond-insulation
+ */
+ 
+process INSULATION {
+  label 'process_medium'
+
+  input:
+  tuple val(meta), path(cool)
+
+  output:
+  path("*tsv"), emit:results
+  path("versions.yml"), emit:versions
+
+  script:
+  def args = task.ext.args ?: ''
+  def prefix = task.ext.prefix ?: "${meta.id}"
+  """
+  cooltools insulation ${cool} ${args} > ${prefix}_insulation.tsv
+
+  cat <<-END_VERSIONS > versions.yml
+  "${task.process}":
+      cooltools: \$(cooltools --version 2>&1 | sed 's/cooltools, version //')
+  END_VERSIONS
+  """
+}

modules/local/tads_insulation.nf

-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options    = initOptions(params.options)
-
-process tads_insulation {
-  tag "$sample - $res"
-  label 'process_medium'
-  publishDir "${params.outdir}/tads/insulation", mode: 'copy'
-
-  when:
-  !params.skip_tads && params.tads_caller =~ 'insulation'
-
-  input:
-  tuple val(sample), val(res), path(cool), val(r) 
-
-  output:
-  path("*tsv"), emit:insulation_tads
-
-  script:
-  """
-  cooltools diamond-insulation --window-pixels ${cool} 15 25 50 > ${sample}_insulation.tsv
-  """
-}

subworkflows/local/compartments.nf

-params.options = [:]
-
-include { COMPARTMENT_CALLING } from '../../modules/local/compartment_calling' addParams( options: params.options )
+include { CALL_COMPARTMENTS } from '../../modules/local/cooltools/eigs-cis'
 
 workflow COMPARTMENTS {
 
-    take:
+  take:
+  cool
+  fasta
+  chrsize
 
+  main:
+  ch_versions = Channel.empty()
 
-    main:
-    
+  CALL_COMPARTMENTS (
+    cool,
+    fasta.collect(),
+    chrsize.collect()
+  )
+  ch_versions = ch_versions.mix(CALL_COMPARTMENTS.out.versions)
 
-    emit:
-    
+  emit:
+  versions = ch_versions
+  compartments = CALL_COMPARTMENTS.out.results
 }
\ No newline at end of file

subworkflows/local/cooler.nf

@@ -8,9 +8,9 @@ include { COOLER_CLOAD } from '../../modules/nf-core/modules/cooler/cload/main'
 include { COOLER_DUMP } from '../../modules/nf-core/modules/cooler/dump/main'
 include { COOLER_ZOOMIFY } from '../../modules/nf-core/modules/cooler/zoomify/main'
 
-include { COOLER_BALANCE } from '../../modules/local/balance'
+include { COOLER_BALANCE } from '../../modules/local/cooler/balance'
 include { SPLIT_COOLER_DUMP } from '../../modules/local/split_cooler_dump'
-include { COOLER_MAKEBINS } from '../../modules/local/makebins'
+include { COOLER_MAKEBINS } from '../../modules/local/cooler/makebins'
 
 workflow COOLER {
 

subworkflows/local/tads.nf

-params.options = [:]
-
-include { TADS_HICEXPLORER } from '../../modules/local/tads_hicexplorer' addParams( options: params.options )
-include { TADS_INSULATION } from '../../modules/local/tads_insulation' addParams( options: params.options )
+include { INSULATION } from '../../modules/local/cooltools/insulation'
+include { HIC_FIND_TADS } from '../../modules/local/hicexplorer/hicFindTADs'
 
 workflow TADS {
 
-    take:
+  take:
+  cool
 
+  main:
+  ch_versions = Channel.empty()
+  ch_tads = Channel.empty()
 
-    main:
-    
+  if (params.tads_caller =~ 'insulation'){
+    INSULATION(cool)
+    ch_versions = ch_versions.mix(INSULATION.out.versions)
+    ch_tads = ch_tads.mix(INSULATION.out.results)
+  }
+  
+  if (params.tads_caller =~ 'hicexplorer'){
+    HIC_FIND_TADS(cool)
+    ch_versions = ch_versions.mix(HIC_FIND_TADS.out.versions)
+    ch_tads = ch_tads.mix(HIC_FIND_TADS.out.results)
+  }
 
-    emit:
-    
+  emit:
+  tads = ch_tads
 }
\ No newline at end of file

workflows/hic.nf

@@ -96,9 +96,9 @@ ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multi
 //
 // MODULE: Local to the pipeline
 //
-//include { GET_SOFTWARE_VERSIONS } from '../modules/local/get_software_versions' addParams( options: [publish_files : ['tsv':'']] )
-//include { OUTPUT_DOCUMENTATION } from '../modules/local/output_documentation' addParams( options: [publish_files : ['tsv':'']] )
-
+//include { GET_SOFTWARE_VERSIONS } from '../modules/local/get_software_versions'
+//include { OUTPUT_DOCUMENTATION } from '../modules/local/output_documentation'
+include { HIC_PLOT_DIST_VS_COUNTS } from '../modules/local/hicexplorer/hicPlotDistVsCounts' 
 //
 // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
 //
@@ -106,8 +106,8 @@ include { INPUT_CHECK } from '../subworkflows/local/input_check'
 include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome'
 include { HICPRO } from '../subworkflows/local/hicpro'
 include { COOLER } from '../subworkflows/local/cooler'
-//include { COMPARTMENTS } from '../subworkflows/local/compartments'
-//include { TADS } from '../subworkflows/local/tads'
+include { COMPARTMENTS } from '../subworkflows/local/compartments'
+include { TADS } from '../subworkflows/local/tads'
 
 /*
 ========================================================================================
@@ -190,6 +190,53 @@ workflow HIC {
     ch_map_res
   )
 
+  //
+  // MODULE: HICEXPLORER/HIC_PLOT_DIST_VS_COUNTS
+  //
+  if (!params.skip_dist_decay){
+    COOLER.out.cool
+      .combine(ch_ddecay_res)
+      .filter{ it[1] == it[3] }
+      .map { it -> [it[0], it[2]]}
+      .set{ ch_distdecay }
+
+    HIC_PLOT_DIST_VS_COUNTS(
+      ch_distdecay
+    )
+  }
+
+  //
+  // SUB-WORKFLOW: COMPARTMENT CALLING
+  //
+  if (!params.skip_compartments){
+    COOLER.out.cool
+      .combine(ch_comp_res)
+      .filter{ it[1] == it[3] }
+      .map { it -> [it[0], it[1], it[2]]}
+      .set{ ch_cool_compartments }
+
+    COMPARTMENTS(
+      ch_cool_compartments,
+      ch_fasta,
+      PREPARE_GENOME.out.chromosome_size
+    )
+  }
+
+  //
+  // SUB-WORKFLOW : TADS CALLING
+  //
+  if (!params.skip_tads){
+    COOLER.out.cool
+      .combine(ch_tads_res)
+      .filter{ it[1] == it[3] }
+      .map { it -> [it[0], it[2]]}
+      .set{ ch_cool_tads }
+                                                                                                                                                                                                            
+    TADS(
+      ch_cool_tads
+    )
+  }
+
   //
   // MODULE: MultiQC
   //